FA-12541 / Genomic coordinate mapping / Open access

Negative-strand transcript offsets visit exons in reference order · case 01

Negative-strand transcript offsets visit exons in reference order.

Verified by executionVariant 1 · 7 checks per implementationDownload source bundle ↓JSON ↗

ROOT CAUSE

Exons are traversed in increasing reference order for both strands.

VERIFIED REPAIR

Reverse exon traversal on the negative strand before consuming transcript offsets.

Unsuccessful approach: Reversing bases within each exon leaves exon traversal wrong.

Case contract

Map zero-based transcript offset across disjoint half-open exons to a reference base; return None outside transcript.

Why this case matters

An abstract offline coordinate model isolates this software mapping defect; it does not model biological interpretation.

1 / The failure

Exit 1

"""Failure Map reference implementation. Python standard library only."""
import json

N = 1
observations = []
def solve(exons, strand, offset):
    for a,b in sorted(exons):
     if 0 <= offset < b-a: return a+offset
     offset -= b-a
    return None
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
e=[(10*N,10*N+2),(10*N+10,10*N+13)]
check('minus first',solve(e,'-',0),10*N+12)
check('minus junction',solve(e,'-',3),10*N+1)
check('minus last',solve(e,'-',4),10*N)
check('plus first',solve(e,'+',0),10*N)
check('plus junction',solve(e,'+',2),10*N+10)
check('past end',solve(e,'-',5),None)
check('negative',solve(e,'+',-1),None)
print(json.dumps({"observations": observations, "passed": all(x["passed"] for x in observations)}, ensure_ascii=False))
raise SystemExit(0 if all(x["passed"] for x in observations) else 1)

Boundary fixture	Actual	Expected	Outcome
minus first	`10`	`22`	Failed
minus junction	`21`	`11`	Failed
minus last	`22`	`10`	Failed
plus first	`10`	`10`	Passed
plus junction	`20`	`20`	Passed
past end	`None`	`None`	Passed
negative	`None`	`None`	Passed

SHA-256 / 098a95cf174c5a5e2afb5175f872250cedb156d47336ce83e699c02bbbf78216

2 / The unsuccessful fix

Exit 1

"""Failure Map reference implementation. Python standard library only."""
import json

N = 1
observations = []
def solve(exons, strand, offset):
    for a,b in sorted(exons):
     if 0 <= offset < b-a: return a+offset if strand=='+' else b-1-offset
     offset -= b-a
    return None
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
e=[(10*N,10*N+2),(10*N+10,10*N+13)]
check('minus first',solve(e,'-',0),10*N+12)
check('minus junction',solve(e,'-',3),10*N+1)
check('minus last',solve(e,'-',4),10*N)
check('plus first',solve(e,'+',0),10*N)
check('plus junction',solve(e,'+',2),10*N+10)
check('past end',solve(e,'-',5),None)
check('negative',solve(e,'+',-1),None)
print(json.dumps({"observations": observations, "passed": all(x["passed"] for x in observations)}, ensure_ascii=False))
raise SystemExit(0 if all(x["passed"] for x in observations) else 1)

Boundary fixture	Actual	Expected	Outcome
minus first	`11`	`22`	Failed
minus junction	`21`	`11`	Failed
minus last	`20`	`10`	Failed
plus first	`10`	`10`	Passed
plus junction	`20`	`20`	Passed
past end	`None`	`None`	Passed
negative	`None`	`None`	Passed

SHA-256 / 31c69ece09aff0504918f5f12d15a271ceaf2bfa16def2fd43ca0cd67c5e5a72

3 / The verified repair

Exit 0

"""Failure Map reference implementation. Python standard library only."""
import json

N = 1
observations = []
def solve(exons, strand, offset):
    for a,b in sorted(exons, reverse=strand=='-'):
     if 0 <= offset < b-a: return a+offset if strand=='+' else b-1-offset
     offset -= b-a
    return None
def check(label, actual, expected):
    observations.append({"check": label, "actual": actual, "expected": expected, "passed": actual == expected})
e=[(10*N,10*N+2),(10*N+10,10*N+13)]
check('minus first',solve(e,'-',0),10*N+12)
check('minus junction',solve(e,'-',3),10*N+1)
check('minus last',solve(e,'-',4),10*N)
check('plus first',solve(e,'+',0),10*N)
check('plus junction',solve(e,'+',2),10*N+10)
check('past end',solve(e,'-',5),None)
check('negative',solve(e,'+',-1),None)
print(json.dumps({"observations": observations, "passed": all(x["passed"] for x in observations)}, ensure_ascii=False))
raise SystemExit(0 if all(x["passed"] for x in observations) else 1)

Boundary fixture	Actual	Expected	Outcome
minus first	`22`	`22`	Passed
minus junction	`11`	`11`	Passed
minus last	`10`	`10`	Passed
plus first	`10`	`10`	Passed
plus junction	`20`	`20`	Passed
past end	`None`	`None`	Passed
negative	`None`	`None`	Passed

SHA-256 / 54abb47e9905e1d02af4e0ce186389801312d0fecd18bc2b8b8b57aaafd2fd2a

Verification & scope

Synthetic coordinate fixtures only; not a production annotation or alignment implementation. This reproducer isolates one failure mechanism. Results cover the supplied fixtures. Variants within a family share a test contract and should remain grouped when constructing evaluation splits. Related mechanisms with a shared evaluation_group must also remain together; these controlled models are not independent production incidents.

Observations recorded using Python 3.12.14 at 2026-09-29T14:38:57.881697+00:00.

Case digest / fd9e4991bba62b265c5968d07b9546183639d8ce98492baafacd17c7a1764bea